A new time-delay estimation (TDE) technique based on dynamic programming is developed to measure the time-varying time-delay between two signals. The dynamic programming based TDE technique provides a frequency response five to ten times better than previously known TDE techniques, namely, those based on time-lag cross-correlation or wavelet analysis. Effects of frequency spectrum, signal-to-noise ratio, and amplitude of time-delay on response of the TDE technique (represented as transfer function) are studied using simulated data signals. The transfer function for the technique decreases with increase in noise in signal; however it is independent of signal spectrum shape. The dynamic programming based TDE technique is applied to the beam emission spectroscopy diagnostic data to measure poloidal velocity fluctuations, which led to the observation of theoretically predicted zonal flows in high-temperature tokamak plasmas.